Table 2.
Quantitative comparison of pan-genome graphs in terms of size and complexity, and the pan-genome content, all run in default configurations, except for the three that also include a different mode
|
Method |
Roary |
Ptolemy |
PPanGGoLin |
PIRATE |
Panaroo |
||
|---|---|---|---|---|---|---|---|
|
Settings |
Default |
Default |
Default |
Defrag |
blast |
Relaxed |
Strict |
|
No. of nodes |
13 928 |
20 140 |
11 329 |
9318 |
7871 |
10 776 |
10 336 |
|
No. of edges |
21 032 |
31 946 |
17 751 |
14 989 |
11 331 |
16 270 |
14 709 |
|
No. of connected components |
10 |
34 |
7 |
6 |
416 |
13 |
13 |
|
Mean sequence length (bp) |
803.7 |
870.5 |
815.5 |
849.8 |
850 |
824.6 |
832.5 |
|
Average no. of genomes per node |
18.7 |
11.7 |
22.4 |
27.1 |
31.6 |
24.4 |
25 |
|
Core genes |
1996 (14.3 %) |
1623 (8.1 %) |
2025 (17.9 %) |
2223 (23.8 %) |
2126 (27 %) |
1910 (17.7 %) |
2353 (22.8 %) |
|
Soft core genes |
429 (3.1 %) |
624 (3.1 %) |
509 (4.5 %) |
389 (4.2 %) |
447 (5.7 %) |
783 (7.3 %) |
322 (3.1 %) |
|
Shell genes |
1912 (13.7 %) |
1367 (6.8 %) |
1624 (14.3 %) |
1526 (16.4 %) |
1516 (19.3 %) |
1655 (15.4 %) |
1609 (15.6 %) |
|
Cloud |
9591 (68.9 %) |
16 526 (82.1 %) |
7171 (63.3 %) |
5180 (55.6 %) |
3782 (48 %) |
6419 (59.6 %) |
6052 (58.5 %) |
|
Unique |
5276 (37.9 %) |
13 963 (69.3%) |
4271 (37.7 %) |
2522 (27.1 %) |
1629 (20.7 %) |
3299 (30.6 %) |
2968 (28.7 %) |